EVOLUTION-MANAGER
Edit File: mqmplotcircle.html
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Circular genome plot for MQM</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for mqmplot.circle {qtl}"><tr><td>mqmplot.circle {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Circular genome plot for MQM</h2> <h3>Description</h3> <p>Circular genome plot - shows QTL locations and relations. </p> <h3>Usage</h3> <pre> mqmplot.circle(cross,result,highlight=0,spacing=25, interactstrength=2, axis.legend=TRUE, col.legend=FALSE, verbose=FALSE, transparency=FALSE) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>cross</code></td> <td> <p>An object of class <code>cross</code> with optionally phenotype locations. See <code><a href="read.cross.html">read.cross</a></code> for details on reading in cross objects, and optionally <code><a href="addloctocross.html">addloctocross</a></code> for adding phenotype locations. </p> </td></tr> <tr valign="top"><td><code>result</code></td> <td> <p>An object of class <code>mqmmulti</code> or <code>scanone</code>. See <code><a href="mqmscanall.html">mqmscanall</a></code> <code><a href="scanone.html">scanone</a></code> for details. </p> </td></tr> <tr valign="top"><td><code>highlight</code></td> <td> <p> With a mqmmulti object, highlight this phenotype (value between one and the number of results in the mqmmultiobject) </p> </td></tr> <tr valign="top"><td><code>interactstrength</code></td> <td> <p> When highlighting a trait, consider interactions significant they have a change of more than interactstrength*SEs. A higher value will show less interactions. However the interactions reported at higher interactstrength values will generaty be more reliable. </p> </td></tr> <tr valign="top"><td><code>spacing</code></td> <td> <p> User defined spacing between chromosomes in cM </p> </td></tr> <tr valign="top"><td><code>axis.legend</code></td> <td> <p> When set to FALSE, suppresses the legends. (defaults to plotting legends besides the axis. </p> </td></tr> <tr valign="top"><td><code>col.legend</code></td> <td> <p> With a mqmmulti object, plots a legend for the non-highlighed version </p> </td></tr> <tr valign="top"><td><code>transparency</code></td> <td> <p> Use transparency when drawing the plots (defaults to no transparency) </p> </td></tr> <tr valign="top"><td><code>verbose</code></td> <td> <p> Be verbose </p> </td></tr> </table> <h3>Details</h3> <p>Depending on the input of the result being either <code><a href="scanone.html">scanone</a></code> or <code>mqmmulti</code> a different plot is drawn. If model information is present from <code><a href="mqmscan.html">mqmscan</a></code> (by setting cofactors) This will be highlighted in red (see example). If phenotypes have genetic locations (e.g. eQTL) they will be plotted on the genome otherwise phenotypes will be plotted in the middle of the circle (with a small offset) Locations can be added by using the <code><a href="addloctocross.html">addloctocross</a></code> function. </p> <h3>Value</h3> <p>Plotting routine, no return </p> <h3>Author(s)</h3> <p>Danny Arends <a href="mailto:danny.arends@gmail.com">danny.arends@gmail.com</a> </p> <h3>See Also</h3> <ul> <li><p> The MQM tutorial: <a href="https://rqtl.org/tutorials/MQM-tour.pdf">https://rqtl.org/tutorials/MQM-tour.pdf</a> </p> </li> <li> <p><code><a href="MQM.html">MQM</a></code> - MQM description and references </p> </li> <li> <p><code><a href="mqmscan.html">mqmscan</a></code> - Main MQM single trait analysis </p> </li> <li> <p><code><a href="mqmscanall.html">mqmscanall</a></code> - Parallellized traits analysis </p> </li> <li> <p><code><a href="mqmaugment.html">mqmaugment</a></code> - Augmentation routine for estimating missing data </p> </li> <li> <p><code><a href="mqmautocofactors.html">mqmautocofactors</a></code> - Set cofactors using marker density </p> </li> <li> <p><code><a href="mqmsetcofactors.html">mqmsetcofactors</a></code> - Set cofactors at fixed locations </p> </li> <li> <p><code><a href="mqmpermutation.html">mqmpermutation</a></code> - Estimate significance levels </p> </li> <li> <p><code><a href="scanone.html">scanone</a></code> - Single QTL scanning </p> </li></ul> <h3>Examples</h3> <pre> data(multitrait) data(locations) multifilled <- fill.geno(multitrait) # impute missing genotypes multicof <- mqmsetcofactors(multitrait,10) # create cofactors multiloc <- addloctocross(multifilled,locations) # add phenotype information to cross multires <- mqmscanall(multifilled,cofactors=multicof) # run mqmscan for all phenotypes #Basic mqmmulti, color = trait, round circle = significant mqmplot.circle(multifilled,multires) #mqmmulti with locations of traits in multiloc mqmplot.circle(multiloc,multires) #mqmmulti with highlighting mqmplot.circle(multitrait,multires,highlight=3) #mqmmulti with locations of traits in multiloc and highlighting mqmplot.circle(multiloc,multires,highlight=3) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>